Contents

real2rgb from File Exchange

12/10/2012

Dear Oliver Woodford,
My name is Juan Pablo Carbajal, I am developer at Octave-Forge[1] a
sibling project of GNU/Octave. I have downloaded your package real2rgb from
the Matlab file exchange and I find it
very useful.
Would you like to contribute it to Octave-Forge? I know licensing issues are
difficult topics and therefore I approach you with utter respect.
If you accept this invitation to contribute code to Octave-Forge, I can
offer
you the following
- You will be properly credited and your papers will be linked as well.
- Maintenance of your function, test and demos will be taken over by the
Octave and Octave-forge community. Of course you can continue contributing,
and we will very happy to have you among us. I will also
let you know of any bug report we get from the users.
- I will take care of porting (code formatting, demos and test).
- You function will be directly downloaded and installed from an
Octave prompt (assuming it is packed inside real2rgb package):
> pkg -forge install real2rgb
The only thing that you need to do is to release your code under GPLv3 (we
like this one :D ) or any license compatible with them, e.g. FreeBSD. I
cannot use the downloaded the packages from the Matlab file exchange because
it will be a violation of their "Terms of Use" (that code can be used only
in
Mathworks products). You need only to let me know that you allow me to
redistribute your code under your free license of choice, I will
take care of adding the header to each file of your package.
In case you are interested, I can tell you about successful experiences of
other researches contributing their work. For example the matGeom
community[2] released under GPLv3 so that Octave-forge can mirror they
package[3], since the package have enjoyed several new contributions and
code
optimization. A group form the technical
university of Denmark[4] working on nonnegative matrix factorization also
allowed us to redistribute their package under GPLv3. Biomechanics &
Neurosciences researchers[5] have also changed their license to GPLv3 to
allow us to produce packages out of their excellent algorithms.
We have no other objective but to offer a truly free platform for the
exchange of our research. I hope you join us!
If you have any question or comments, please let me know without hesitation.
Thank you very much for your excellent code!
Regards,
[1] http://octave.sourceforge.net/
[2] http://sourceforge.net/apps/mediawiki/matgeom/index.php?title=Main_Page
[3] http://www.octave.org/wiki/index.php?title=Geometry_package
[4] http://cogsys.imm.dtu.dk/toolbox/nmf/index.html
[5]
http://sites.google.com/site/systemsneurosciencegroup/people/stewart-heitmann

Gaussian Processes for machine learning

21/5/2012

Dear Dr. Nickisch and Dr. Rasmussen,
My name is Juan Pablo Carbajal, I am developer at Octave-Forge[1] a
sibling project of GNU/Octave. I
have downloaded your package gpml-v3.1 from your website and I find it
very useful (also fan of your book GP for ML).
Would you like to contribute it to Octave-Forge? I know licensing
issues are difficult topics and therefore I approach you with utter
respect.
If you accept this invitation to contribute code to Octave-Forge, I
can offer you the following
- You will be properly credited and your papers will be linked as well.
- Maintenance of your function, test and demos will be taken over by
the Octave and Octave-forge community. Of course you can continue
contributing, and we will very happy to have you among us. I will also
let you know of any bug report we get from the users.
- I will take care of code formatting, demos and test.
- You function will be directly downloaded and installed from an
Octave terminal (assuming it is packed inside gaussp package):
>pkg -forge install gaussp
The only thing that you need to do is to release your code under GPLv3
(we like this one :D ) or any license compatible with them, e.g.
FreeBSD. Although the current license of your package is quite free,
it is a custom license
and GNU wouldn't accept it. You need only to let me know that you
allow me to redistribute your code under your free license of choice, I will
take care of adding the header to each file of your package.
In case you are interested, I can tell you about successful
experiences of other researches contributing their work. For
example the Matgeom community[2] released under GPLv3 so that
Octave-forge can mirror they package[3], since the package have
enjoyed several new contributions and code optimization. A group form
the technical
university of Denmark[4] working on nonnegative matrix factorization
also allowed us to
redistribute their package under GPLv3. Biomechanics & Neurosciences
researchers[5] have also changed their license to GPLv3 to allow us to
produce packages out of their excellent algorithms.
We have no other objective but to offer a truly free platform for the
exchange of our research. I hope
you join us!
If you have any question or comments, please let me know without hesitation.
Thank you very much for your excellent code (and book!)
[1] http://octave.sourceforge.net/
[2] http://sourceforge.net/apps/mediawiki/matgeom/index.php?title=Main_Page
[3] http://www.octave.org/wiki/index.php?title=Geometry_package
[4] http://cogsys.imm.dtu.dk/toolbox/nmf/index.html
[5] http://sites.google.com/site/systemsneurosciencegroup/people/stewart-heitmann

SPM ID Toolbox

7/1/2011

Dear Brett,
Thank you very much for your toolbox.
I am trying to run it in Octave 3.5.0+ and it doesn't work. On one
side the control functions of octave have been updated and the old
ones (that apparently are dumped by Mathworks in the signal toolbox)
were removed, but I am working on it. On the other side, I found some
bugs in your package.
For example, the function rksqrtv.m is empty! which makes demo_unit
option 19 fail. However, even if the function were there, with the
interface as explained in the help, then ks.m would produce an error
at the end, because the matrix G has no field called ss.
Another bug I found in m2f line 165. The output of mimofr would be of
size number-of-ouputs x number-of-inputs x number-of-frequencies. As
it is used there, the addition will fail for the option 20 of
demo_unit I corrected by doing
G.H=mimofr(G.ss.A,G.ss.K,G.ss.C,[],ww);
DK = eye(size(G.H,1),size(G.H,2));
G.H=G.H + DK(:,:,ones(1,length(ww)));
by the way, if you were aiming to make UNIT compatible with Octave
3.5.0+, you would have freqresp.m available in the control package.
Are you planning to produce an Octave 3.5.0+ compatible version of
your excellent package?
Thanks again,
Regards,

12/9/2012

Dear Brett Ninness,
I am writing you once more in relation to the SPM toolbox
(http://sigpromu.org/idtoolbox/).
GNU Octave is now in its 3.6.x version and the packages are
experiencing fast development. Take for example (and most related to
your package) the control package
(http://octave.sourceforge.net/control/overview.html). You may notice
under the section "Experimental data handling" and "System
identification" some interesting new functionality.
Do you have plans to release your package under a GPL compatible
license (http://en.wikipedia.org/wiki/List_of_FSF-approved_software_licenses)?
Only under this licesing scheme we can include and extended your
package into GNU Octave packages. It may be advantageous, in terms of
visibility and use, to release a free version that can be shipped with
GNU Octave packages, since users can download it and install it
directly from the prompt. Additionally, the packages that are most
popular are shipped within Linux distributions like Debian and Fedora.
Please let us know about your decision.
Thank you very much in advance.
Kind regards,

Non-negative matrix factorization

9/3/2012

Dear Dr. Jingu Kim,
My name is Juan Pablo Carbajal, I am a developer of Octave-Forge[1]. I
have downloaded your package nmf_bpas from your website and I find it
very useful.
Would you like to contribute it to Octave-Forge? I know licensing
issues are difficult topics and therefore I approach you with utter
respect.
If you accept this invitation to contribute code to Octave-Forge, I
can offer you the following
- You will be properly credited and your papers will be linked as well.
- Maintenance of your function, test and demos will be taken over by
the Octave and Octave-forge community. Of course you can continue
contributing, and we will very happy to have you among us.
- I will take care of code formatting, demos and test.
- You function will be directly downloaded and installed form an
Octave terminal (assuming it is packed inside linear-algebra package):
>pkg -forge install linear-algebra
The only thing that you need to do is to release your code under GPLv3
(we like this one :D ) or any license compatible with them, e.g.
FreeBSD. We already have an algorithm for nmf, by Chih-Jen Lin[2] but
we would like to have a good variety of implementations, therefore we
ask for your contribution.
In case you are interested, I can tell you about successful
experiences of together researches contributing their work. For
example the Matgeom community[3] released under GPLv3 so that
Octave-forge can mirror they package[4]. Biomechanics & Neurosciences
researchers[5] have also changed their license to GPLv3 to allow us to
produce packages out of their excellent algorithms. We are trying to
offer a truly free platform for the exchange of our research. I hope
you join us!
[1] http://octave.sourceforge.net/
[2] http://www.csie.ntu.edu.tw/~cjlin/nmf/index.html
[3] http://sourceforge.net/apps/mediawiki/matgeom/index.php?title=Main_Page
[4] http://www.octave.org/wiki/index.php?title=Geometry_package
[5] http://sites.google.com/site/systemsneurosciencegroup/people/stewart-heitmann
Looking forward to your answer,
Best regards,

Dear Chih-Jen Lin,
My name is Juan Pablo Carbajal, I am a developer of Octave-Forge[1]. I
have downloaded your function nmf.m from your website and I find it
very useful.
Would you like to contribute it to Octave-Forge? I know licensing
issues are difficult topics and therefore I approach you with utter
respect.
If you accept this invitation to contribute code to Octave-Forge, I
can offer you the following
- You will be properly credited and your papers will be linked as well.
- Maintenance of your function, test and demos will be taken over by
the Octave and Octave-forge community. Of course you can continue
contributing, and we will very happy to have you among us.
- I will take care of code formatting, demos and test.
- You function will be directly downloaded and installed form an
Octave terminal (assuming it is packed inside linear-algebra package):
>pkg -forge install linear-algebra
The only thing that you need to do is to release your code under GPLv3
(we like this one :D ) or any license compatible with them, e.g.
FreeBSD.
In case you are interested, I can tell you about successful
experiences of together researches contributing their work. For
example the Matgeom community[2] released under GPLv3 so that
Octave-forge can mirror they package[3]. Biomechanics & Neurosciences
researchers[4] have also changed their license to GPLv3 to allow us to
produce packages out of their excellent algorithms. We are trying to
offer a truly free platform for the exchange of our research. I hope
you join us!
Looking forward to your answer,
Best regards,

27/3/2012

Dear Kasper Winther Joergensen,
My name is Juan Pablo Carbajal, I am a developer of Octave-Forge[1]. I have downloaded the nmf toolbox 1-4-0 from your website and I find it very useful.
Would you like to contribute it to Octave-Forge? I know licensing issues are difficult topics and therefore I approach you with utter respect.
If you accept this invitation to contribute code to Octave-Forge, I can offer you the following
- You will be properly credited and your papers will be linked as well.
- Maintenance of your toolbox, test and demos will be taken over by the Octave and Octave-forge community. Of course you can continue contributing, and we will very happy to have you among us.
- I will take care of code formatting, demos and test.
- You function will be directly downloaded and installed form an Octave terminal (assuming it is packed inside linear-algebra package):
>pkg -forge install linear-algebra
The only thing that you need to do is to release your code under GPLv3 (we like this one :D ) or any license compatible with them, e.g.
FreeBSD. Chih-Jen Lin (author of the file nmf_cjlin in your toolbox) and Jingu Kim have already send me their permission to post their code in Octave-Forge. I hope you join us!
In case you are interested, I can tell you about successful experiences of together researches contributing their work. For example the Matgeom community[2] released under GPLv3 so that Octave-forge can mirror they package[3]. Biomechanics & Neurosciences researchers[4] have also changed their license to GPLv3 to allow us to produce packages out of their excellent algorithms. We are trying to offer a truly free platform for the exchange of our research.
Looking forward to your answer,
Best regards,

Motion tracking

29/8/2012

Dear Marie Dacke and Emily Baird,
Thank you once more for your interesting research and motivating
presentation about dung beetles.
As we discussed post-processing the data recorded with cameras and
tracking the position of the bugs is time consuming. Automatizing and
standardizing this task is very important for reproducible research
and the speed up development in ethology.
You told me that you post-process your movies using Matlab. I would
like to port your scripts to GNU Octave to make them completely free
(that is the code can be run in free software). If you could provide
some of your code so I can test it in Octave, it would be very
helpful. We will see what developments are needed in the current
version of Octave and the community will work on that.
To be useful in Octave we would need that the code you send is
released under a free license (we refer GPLv3, but any in the column
GPL compatible would do fine
http://en.wikipedia.org/wiki/List_of_FSF_approved_software_licenses).
Your authorship will never be removed form the files, only editors
names will be added if required.
Looking forward to work on your code.
Sincerely

Biomechanical muscle models

21/12/2011

Dear Stewart,
Thank you again for establishing the contact.
From the latest video I understand that the torques generated in
joints closer to the "shoulder" due to the segments farther away,
change the stability of some of the equilibrium points. If that is the
case this is something that one cannot predict studying isolated
links. However, I guess that studying isolated links with an extra
constant term would show these bifurcations as well (that is, the
torque due to its own weight + some external constant torque).
I have an interest in your work since my work is related. In my thesis
I study the effect that body properties (around here people speaks of
"morphology") may have on the difficulty of performing certain tasks.
Stated as a question, Can we quantify the relation between function
and morphology? I studied several cases and one of them is kinematic
chains, though I did not achieve a strong answer to the question I
came up with a method to calculate solution to control problems base
don the natural dynamics of the kinematic chain. Using models as the
one you report in your paper is of high interest to me (but for an
after thesis life, i.e. ~July 2012). Maybe we can have a sort of
collaboration there. I am collaborating with Andrea d'Avella (context
of AMARSi project[0]) and with a student of Francesco Nori, I guess it
will be great to unite forces ;D.
Additionally, I plan to release my algorithms in a package (probably
named biomechanics) for Octave[1,2] (I hope you know it, is very
similar to Matlab) and I was wondering if you would like to release
yours as well, in the same package. The only formal requirement is
that your code has a GNU compatible license (FreeBSD, GPL, LGPL, etc).
I am already a developer there, so I could take care of the
"administrative" burden. Here [3] you can see my TODO list for Octave,
to see what is to come (for example the robotics package!)
Looking forward to your answer!
[0] http://www.amarsi-project.eu/
[1] http://www.gnu.org/software/octave/
[2] http://octave.sourceforge.net/
[3] http://octave.org/wiki/index.php?title=User:KaKiLa

matGeom

26/9/2011

Dear David,
I would like to discuss the possibility of making matGeom compatible
with Octave and upload it to the Octave-Packages server.
http://octave.sourceforge.net/index.html
Packages there are maintained individually and people can get them
directly from inside octave. That make is really easy to install the
package.
Regarding the license. You can release your code with multiple
licenses, that is not a problem at all. If you add the GPL version to
a zip and send it, then that code will be GPL. Nevertheless BSD work
fine as well. Just let me know when you add the license (make sure you
add 3-clause or 2-clause BSD
(http://en.wikipedia.org/wiki/BSD_licenses), otherwise we cannot add
it to Octave).
As soon as you let me know, I will start the upload.
Thanks
Regards,